Automatic Case Creation from ICA - Cyto Array Analysis

Overview

This feature enables automatic case creation in EMG following the successful completion of specific array analysis events on ICA. The automation supports efficient and standardized case generation, ensuring timely downstream review and interpretation.

When It Applies

This feature is triggered when a DRAGEN Array - Cyto CNV calling with Emedgene tertiary interpretation analysis is completed successfully on ICA.

Prerequisites

Before automatic case creation can occur, ensure the following conditions are met:

1. The user needs to have access to BSSH and Emedgene in the same workgroup.

2. The managed ICA project must be connected to the EMG workgroup:

   • The managed ICA project needs to be the one was created automatically by BSSH after running the first analysis (BSSH {workgroup name}, for example "BSSH MyWG").

   • This ensures EMG has access to the analysis outputs and metadata from the managed ICA project.

3. Enabling ICA Notifications for the BSSH Project:

   To ensure proper integration with EMG, ICA notifications must be enabled for the specific BSSH project. EMG relies on these notifications to detect when an analysis has successfully completed.

   To configure an SNS notification in your managed ICA project, follow these steps:

   • In the ICA portal, in the managed project, navigate to the Notifications section via the left-hand menu.

   

   • Click + Create, then select ICA Event.

   

   • Fill in the required fields as follows:

     • Event: Analysis Success

     • Type: SNS

     • Address: Provide the correct address based on your region (contact support if unsure).

     • Payload Version: v4

     • AWS Region: This will be auto-populated based on the provided address.

     • (Recommended) Click Send Test Message to verify the configuration.

     • Click Save to complete the setup.

   
4. Run a BSSH analysis according to the DRAGEN Array user guide

Automatic Case Creation Workflow

Upon successful analysis completion, the system will:

1. Create a New Case in EMG

   • Case Type: Set to Array.

     • Note: No ROI file will be associated with the case.

   • Sample Type: Set to VCF.

   • Phenotype: Automatically marked as Healthy, with no phenotypes assigned.

2. Attach Files to the Case Each automatically generated case will include:

   • VCF file (mandatory)

   • Visualization files:

     • LRR bedgraph

     • BAF bedgraph

   • gt_summary JSON file (containing metadata and quality information)

3. Extract and Apply Metadata from Sample Sheet

   • If available, Gender/Sex is extracted and applied to the case.

   • If not available, the case is labeled as Sex: Unknown.

4. Exclude Failed Analyses

   • Analyses marked as failed will not trigger case creation in EMG.

Limitations

Please note the following limitations of the automatic case creation feature:

1. Supports only singleton cases

   • Cases involving multiple individuals (e.g., trios or families) are not supported.

2. No phenotype support

   • All cases will be marked as Healthy, with no phenotypes included, regardless of the sample metadata.

Benefits

• Streamlined and seamless workflow between ICA and EMG.

• Reduces manual intervention and potential for data entry errors.